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- PDB-9b0n: In situ human Post-eEF1A-AT-P state 80S ribosome -

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Open data

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Basic information

Entry

Database: PDB / ID: 9b0n

Title

In situ human Post-eEF1A-AT-P state 80S ribosome

Components

(40S ribosomal protein ...) x 22
(60S ribosomal protein ...) x 39
(Large ribosomal subunit protein ...) x 4
(Small ribosomal subunit protein ...) x 9
18S rRNA
28S rRNA
5.8S rRNA
5S rRNA
60S acidic ribosomal protein P0
A/T site tRNA
Elongation factor 1-alpha 1
Heparin-binding protein HBp15
P site tRNA
Receptor of activated protein C kinase 1
Ubiquitin-40S ribosomal protein S27a

Keywords

RIBOSOME / In situ

Function / homology

Function and homology information

cytoplasmic side of lysosomal membrane / Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / positive regulation by host of viral genome replication / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist ...cytoplasmic side of lysosomal membrane / Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / positive regulation by host of viral genome replication / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / axial mesoderm development / negative regulation of peptidyl-serine phosphorylation / positive regulation of respiratory burst involved in inflammatory response / ribosomal protein import into nucleus / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein-DNA complex disassembly / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / translation at postsynapse / kinase activator activity / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / mammalian oogenesis stage / GAIT complex / A band / positive regulation of DNA damage response, signal transduction by p53 class mediator / supercoiled DNA binding / activation-induced cell death of T cells / TORC2 complex binding / G1 to G0 transition / NF-kappaB complex / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / translation at presynapse / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of phagocytosis / erythrocyte homeostasis / rRNA modification in the nucleus and cytosol / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / protein kinase A binding / cortical actin cytoskeleton / negative regulation of ubiquitin protein ligase activity / pigmentation / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / homeostatic process / Translation initiation complex formation / response to aldosterone / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / positive regulation of activated T cell proliferation / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / lung morphogenesis / monocyte chemotaxis / negative regulation of translational frameshifting / Protein hydroxylation / BH3 domain binding / TOR signaling / SARS-CoV-1 modulates host translation machinery / regulation of cell division / mTORC1-mediated signalling / T cell proliferation involved in immune response / Peptide chain elongation / iron-sulfur cluster binding / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / translational elongation / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / blastocyst development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / phagocytic cup / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
Similarity search - Function

Translation elongation factor EF1A, eukaryotic/archaeal / : / GTP-eEF1A C-terminal domain-like / : / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus ...Translation elongation factor EF1A, eukaryotic/archaeal / : / GTP-eEF1A C-terminal domain-like / : / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1 signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L1 / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L44e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / : / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein S27e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4, C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4 C-terminus
Similarity search - Domain/homology

: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS4, X isoform / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Elongation factor 1-alpha 1 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL36
Similarity search - Component

Biological species

Homo sapiens (human)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å

Authors

Wei, Z. / Yong, X.

Funding support

1items

Citation

Journal: To Be Published
Title: In situ human Post-eEF1A-AT-P state 80S ribosome
Authors: Wei, Z. / Yong, X.

History

Deposition	Mar 12, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release
Revision 1.0	Apr 30, 2025	Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0	Apr 30, 2025	Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0	Apr 30, 2025	Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0	Apr 30, 2025	Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0	Apr 30, 2025	Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0	Apr 30, 2025	Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	9b0n.cif.gz	5.5 MB	Display	PDBx/mmCIF format
PDB format	pdb9b0n.ent.gz		Display	PDB format
PDBx/mmJSON format	9b0n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/9b0n ftp://data.pdbj.org/pub/pdb/validation_reports/b0/9b0n	HTTPS FTP

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Related structure data

Related structure data	44047MC M: map data used to model this data C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (94) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (18) #10 - Oct 2000 Ribosome similarity (74) #253 - Jan 2021 Expressome similarity (6) #260 - Aug 2021 Ribonuclease P similarity (8) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #161 - May 2013 Ricin similarity (226) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #60 - Dec 2004 Ubiquitin similarity (83) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (101) #245 - May 2020 Spliceosomes similarity (8) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (3) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (3) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (79) #81 - Sep 2006 Elongation Factors similarity (9) #230 - Feb 2019 Initiation Factor eIF4E similarity (8) #104 - Aug 2008 Selenocysteine Synthase similarity (8) #227 - Nov 2018 Telomerase similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (5) #143 - Nov 2011 Toll-like Receptors similarity (5) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #122 - Feb 2010 Enhanceosome similarity (7) #88 - Apr 2007 Clathrin similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (6) #150 - Jun 2012 Sliding Clamps similarity (5) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (8) #68 - Aug 2005 Neurotrophins similarity (3) #43 - Jul 2003 Src Tyrosine Kinase similarity (3) #56 - Aug 2004 Caspases similarity (3) #165 - Sep 2013 Designed Protein Cages similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #86 - Feb 2007 Exosomes similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #163 - Jul 2013 HIV Capsid similarity (2) #91 - Jul 2007 Thymine Dimers similarity (1) #128 - Aug 2010 Interferons similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (2) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Assembly

Deposited unit

AT: A/T site tRNA

CF: Elongation factor 1-alpha 1

LW: 60S ribosomal protein L24

SE: Small ribosomal subunit protein eS4, X isoform

SI: 40S ribosomal protein S8

SL: 40S ribosomal protein S11

SX: 40S ribosomal protein S23

SG: 40S ribosomal protein S6

SJ: 40S ribosomal protein S9

SY: 40S ribosomal protein S24

Se: Small ribosomal subunit protein eS30

SA: 40S ribosomal protein SA

SB: 40S ribosomal protein S3a

SH: 40S ribosomal protein S7

SV: 40S ribosomal protein S21

Sa: 40S ribosomal protein S26

SC: 40S ribosomal protein S2

SN: 40S ribosomal protein S13

SO: Small ribosomal subunit protein uS11

SW: 40S ribosomal protein S15a

Sb: Small ribosomal subunit protein eS27

L5: 28S rRNA

L7: 5S rRNA

L8: 5.8S rRNA

LA: 60S ribosomal protein L8

LB: Large ribosomal subunit protein uL3

LC: 60S ribosomal protein L4

LD: Large ribosomal subunit protein uL18

LE: 60S ribosomal protein L6

LF: 60S ribosomal protein L7

LG: 60S ribosomal protein L7a

LH: 60S ribosomal protein L9

LI: 60S ribosomal protein L10-like

LJ: 60S ribosomal protein L11

LL: Large ribosomal subunit protein eL13

LM: 60S ribosomal protein L14

LN: 60S ribosomal protein L15

LO: 60S ribosomal protein L13a

LP: 60S ribosomal protein L17

LQ: 60S ribosomal protein L18

LR: 60S ribosomal protein L19

LS: 60S ribosomal protein L18a

LT: 60S ribosomal protein L21

LU: Heparin-binding protein HBp15

LV: 60S ribosomal protein L23

LX: 60S ribosomal protein L23a

LY: 60S ribosomal protein L26

LZ: 60S ribosomal protein L27

La: 60S ribosomal protein L27a

Lb: 60S ribosomal protein L29

Lc: 60S ribosomal protein L30

Ld: 60S ribosomal protein L31

Le: 60S ribosomal protein L32

Lf: 60S ribosomal protein L35a

Lg: 60S ribosomal protein L34

Lh: 60S ribosomal protein L35

Li: 60S ribosomal protein L36

Lj: 60S ribosomal protein L37

Lk: 60S ribosomal protein L38

Ll: 60S ribosomal protein L39

Lm: Large ribosomal subunit protein eL40

Ln: 60S ribosomal protein L41

Lo: 60S ribosomal protein L36a

Lp: 60S ribosomal protein L37a

Lr: 60S ribosomal protein L28

SR: 40S ribosomal protein S17

SD: Small ribosomal subunit protein uS3

SF: 40S ribosomal protein S5

SK: 40S ribosomal protein S10

SP: Small ribosomal subunit protein uS19

SQ: Small ribosomal subunit protein uS9

SS: 40S ribosomal protein S18

ST: 40S ribosomal protein S19

SU: 40S ribosomal protein S20

Sc: 40S ribosomal protein S28

Sd: 40S ribosomal protein S29

Sg: Receptor of activated protein C kinase 1

SM: Small ribosomal subunit protein eS12

SZ: Small ribosomal subunit protein eS25

Sf: Ubiquitin-40S ribosomal protein S27a

S2: 18S rRNA

Pt: P site tRNA

Lz: 60S ribosomal protein L10a

Ls: 60S acidic ribosomal protein P0

Lt: 60S ribosomal protein L12

hetero molecules

3.34 MDa, 85 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Idetical with deposited unit
defined by author
Evidence: electron microscopy, not applicable

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Components

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RNA chain , 6 types, 6 molecules ATL5L7L8S2Pt

#1: RNA chain	A/T site tRNA Mass: 24765.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#22: RNA chain	28S rRNA Mass: 1211748.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#23: RNA chain	5S rRNA Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#24: RNA chain	5.8S rRNA Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1142736641
#81: RNA chain	18S rRNA Mass: 561332.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#82: RNA chain	P site tRNA Mass: 24483.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein , 5 types, 5 molecules CFLUSgSfLs

#2: Protein	Elongation factor 1-alpha 1 Mass: 48247.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68104
#44: Protein	Heparin-binding protein HBp15 Mass: 11722.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z4W8
#77: Protein	Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1 Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#80: Protein	Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80 Mass: 7884.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#84: Protein	60S acidic ribosomal protein P0 / 60S ribosomal protein L10E / Large ribosomal subunit protein uL10 Mass: 21507.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05388

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60S ribosomal protein ... , 39 types, 39 molecules LWLALCLELFLGLHLILJLMLNLOLPLQLRLSLTLVLXLYLZLaLbLcLdLeLfLgLhLi...

#3: Protein	60S ribosomal protein L24 Mass: 13761.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#25: Protein	60S ribosomal protein L8 / Large ribosomal subunit protein uL2 Mass: 26998.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#27: Protein	60S ribosomal protein L4 / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4 Mass: 41747.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#29: Protein	60S ribosomal protein L6 Mass: 27030.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#30: Protein	60S ribosomal protein L7 / Large ribosomal subunit protein uL30 Mass: 26590.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#31: Protein	60S ribosomal protein L7a / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3 Mass: 27452.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#32: Protein	60S ribosomal protein L9 / Large ribosomal subunit protein uL6 Mass: 21655.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#33: Protein	60S ribosomal protein L10-like Mass: 23322.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#34: Protein	60S ribosomal protein L11 / CLL-associated antigen KW-12 / Large ribosomal subunit protein uL5 Mass: 20086.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#36: Protein	60S ribosomal protein L14 / CAG-ISL 7 / Large ribosomal subunit protein eL14 Mass: 16220.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#37: Protein	60S ribosomal protein L15 / Large ribosomal subunit protein eL15 Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#38: Protein	60S ribosomal protein L13a / 23 kDa highly basic protein / Large ribosomal subunit protein uL13 Mass: 23431.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#39: Protein	60S ribosomal protein L17 / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1 Mass: 17757.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#40: Protein	60S ribosomal protein L18 / Large ribosomal subunit protein eL18 Mass: 21556.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#41: Protein	60S ribosomal protein L19 / Large ribosomal subunit protein eL19 Mass: 22441.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#42: Protein	60S ribosomal protein L18a / Large ribosomal subunit protein eL20 Mass: 20677.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#43: Protein	60S ribosomal protein L21 / Large ribosomal subunit protein eL21 Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#45: Protein	60S ribosomal protein L23 / 60S ribosomal protein L17 / Large ribosomal subunit protein uL14 Mass: 13972.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#46: Protein	60S ribosomal protein L23a / Large ribosomal subunit protein uL23 Mass: 13985.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#47: Protein	60S ribosomal protein L26 / Large ribosomal subunit protein uL24 Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#48: Protein	60S ribosomal protein L27 / Large ribosomal subunit protein eL27 Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#49: Protein	60S ribosomal protein L27a / Large ribosomal subunit protein uL15 Mass: 16473.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#50: Protein	60S ribosomal protein L29 Mass: 12630.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#51: Protein	60S ribosomal protein L30 / Large ribosomal subunit protein eL30 Mass: 10954.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#52: Protein	60S ribosomal protein L31 / Large ribosomal subunit protein eL31 Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#53: Protein	60S ribosomal protein L32 / Large ribosomal subunit protein eL32 Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#54: Protein	60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33 Mass: 12433.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#55: Protein	60S ribosomal protein L34 / Large ribosomal subunit protein eL34 Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#56: Protein	60S ribosomal protein L35 / Large ribosomal subunit protein uL29 Mass: 14462.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#57: Protein	60S ribosomal protein L36 / Large ribosomal subunit protein eL36 Mass: 11915.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#58: Protein	60S ribosomal protein L37 / G1.16 / Large ribosomal subunit protein eL37 Mass: 10090.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#59: Protein	60S ribosomal protein L38 / Large ribosomal subunit protein eL38 Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#60: Protein/peptide	60S ribosomal protein L39 / Large ribosomal subunit protein eL39 Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#62: Protein/peptide	60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41 Mass: 3344.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945
#63: Protein	60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 ...60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein / Large ribosomal subunit protein eL42 Mass: 12345.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#64: Protein	60S ribosomal protein L37a / Large ribosomal subunit protein eL43 Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#65: Protein	60S ribosomal protein L28 / Large ribosomal subunit protein eL28 Mass: 14320.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#83: Protein	60S ribosomal protein L10a / CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down- ...CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6 Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62906
#85: Protein	60S ribosomal protein L12 Mass: 15080.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Small ribosomal subunit protein ... , 9 types, 9 molecules SESeSOSbSDSPSQSMSZ

#4: Protein	Small ribosomal subunit protein eS4, X isoform / 40S ribosomal protein S4 / SCR10 / Single copy abundant mRNA protein Mass: 29523.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#11: Protein	Small ribosomal subunit protein eS30 / 40S ribosomal protein S30 Mass: 6539.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#19: Protein	Small ribosomal subunit protein uS11 / 40S ribosomal protein S14 Mass: 15014.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#21: Protein	Small ribosomal subunit protein eS27 / 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 Mass: 9348.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#67: Protein	Small ribosomal subunit protein uS3 Mass: 25172.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P23396
#70: Protein	Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein Mass: 14092.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#71: Protein	Small ribosomal subunit protein uS9 / 40S ribosomal protein S16 Mass: 16249.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#78: Protein	Small ribosomal subunit protein eS12 / 40S ribosomal protein S12 Mass: 13652.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#79: Protein	Small ribosomal subunit protein eS25 / 40S ribosomal protein S25 Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851

+
40S ribosomal protein ... , 22 types, 22 molecules SISLSXSGSJSYSASBSHSVSaSCSNSWSRSFSKSSSTSUScSd

#5: Protein	40S ribosomal protein S8 / Small ribosomal subunit protein eS8 Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#6: Protein	40S ribosomal protein S11 / Small ribosomal subunit protein uS17 Mass: 17785.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#7: Protein	40S ribosomal protein S23 / Small ribosomal subunit protein uS12 Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#8: Protein	40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6 Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#9: Protein	40S ribosomal protein S9 / Small ribosomal subunit protein uS4 Mass: 21649.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#10: Protein	40S ribosomal protein S24 / Small ribosomal subunit protein eS24 Mass: 15203.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#12: Protein	40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2 Mass: 24774.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#13: Protein	40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1 Mass: 24888.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#14: Protein	40S ribosomal protein S7 Mass: 21257.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#15: Protein	40S ribosomal protein S21 / Small ribosomal subunit protein eS21 Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#16: Protein	40S ribosomal protein S26 / Small ribosomal subunit protein eS26 Mass: 11742.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#17: Protein	40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5 Mass: 24587.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#18: Protein	40S ribosomal protein S13 / Small ribosomal subunit protein uS15 Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#20: Protein	40S ribosomal protein S15a / Small ribosomal subunit protein uS8 Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#66: Protein	40S ribosomal protein S17 / Small ribosomal subunit protein eS17 Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#68: Protein	40S ribosomal protein S5 / Small ribosomal subunit protein uS7 Mass: 21327.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#69: Protein	40S ribosomal protein S10 / Small ribosomal subunit protein eS10 Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#72: Protein	40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13 Mass: 17029.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#73: Protein	40S ribosomal protein S19 / Small ribosomal subunit protein eS19 Mass: 15822.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#74: Protein	40S ribosomal protein S20 / Small ribosomal subunit protein uS10 Mass: 11765.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#75: Protein	40S ribosomal protein S28 / Small ribosomal subunit protein eS28 Mass: 7263.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#76: Protein	40S ribosomal protein S29 / Small ribosomal subunit protein uS14 Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273

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Large ribosomal subunit protein ... , 4 types, 4 molecules LBLDLLLm

#26: Protein	Large ribosomal subunit protein uL3 Mass: 46079.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#28: Protein	Large ribosomal subunit protein uL18 Mass: 34008.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#35: Protein	Large ribosomal subunit protein eL13 Mass: 24190.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#61: Protein	Large ribosomal subunit protein eL40 / 60S ribosomal protein L40 Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987

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Non-polymers , 2 types, 261 molecules

#86: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 255 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#87: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experimental details

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Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component	Name: In situ human Post-eEF1A-AT-P state 80S ribosome / Type: RIBOSOME / Entity ID: #1-#85 / Source: NATURAL
Source (natural)	Organism: Homo sapiens (human)
Buffer solution	pH: 7.4
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification	Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Model: FEI TITAN KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recording	Electron dose: 50 e/Å² / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software	Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correction	Type: NONE
3D reconstruction	Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60393 / Symmetry type: POINT

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RNA chain , 6 types, 6 molecules ATL5L7L8S2Pt

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Protein , 5 types, 5 molecules CFLUSgSfLs

+
60S ribosomal protein ... , 39 types, 39 molecules LWLALCLELFLGLHLILJLMLNLOLPLQLRLSLTLVLXLYLZLaLbLcLdLeLfLgLhLi...

-
Small ribosomal subunit protein ... , 9 types, 9 molecules SESeSOSbSDSPSQSMSZ

+
40S ribosomal protein ... , 22 types, 22 molecules SISLSXSGSJSYSASBSHSVSaSCSNSWSRSFSKSSSTSUScSd

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Large ribosomal subunit protein ... , 4 types, 4 molecules LBLDLLLm

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Non-polymers , 2 types, 261 molecules

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Details

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Experimental details

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Experiment

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-RNA chain , 6 types, 6 molecules ATL5L7L8S2Pt

-Protein , 5 types, 5 molecules CFLUSgSfLs

+60S ribosomal protein ... , 39 types, 39 molecules LWLALCLELFLGLHLILJLMLNLOLPLQLRLSLTLVLXLYLZLaLbLcLdLeLfLgLhLi...

-Small ribosomal subunit protein ... , 9 types, 9 molecules SESeSOSbSDSPSQSMSZ

+40S ribosomal protein ... , 22 types, 22 molecules SISLSXSGSJSYSASBSHSVSaSCSNSWSRSFSKSSSTSUScSd

-Large ribosomal subunit protein ... , 4 types, 4 molecules LBLDLLLm

-Non-polymers , 2 types, 261 molecules

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RNA chain , 6 types, 6 molecules ATL5L7L8S2Pt

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Protein , 5 types, 5 molecules CFLUSgSfLs

+
60S ribosomal protein ... , 39 types, 39 molecules LWLALCLELFLGLHLILJLMLNLOLPLQLRLSLTLVLXLYLZLaLbLcLdLeLfLgLhLi...

-
Small ribosomal subunit protein ... , 9 types, 9 molecules SESeSOSbSDSPSQSMSZ

+
40S ribosomal protein ... , 22 types, 22 molecules SISLSXSGSJSYSASBSHSVSaSCSNSWSRSFSKSSSTSUScSd

-
Large ribosomal subunit protein ... , 4 types, 4 molecules LBLDLLLm

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Non-polymers , 2 types, 261 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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